Abstract:    Objective    To compare and analyze single nucleotide polymorphism (SNP) and alternative splicing (AS) between the fresh and vitrified-thawed crossbred blastocysts of the yak. Methods    The crossbred blastocysts were derived from yak oocytes in vitro fertilized with Jersey cattle spermatozoa. Total RNA was extracted from these fresh blastocysts (FRB) and vitrified-thawed blastocysts (VTB), and then amplified and sequenced via the Smart-Seq2 method to construct RNA libraries. SNP and AS were analyzed by SAMtools-0.1.19 and ASprofile software, respectively. Results    A total of 51 099 116 and 54 192 358 clean reads were obtained from the FRB and VTB, respectively. The SNP numbers of FRB and VTB were 116 681 and 224 750, the number of C/T type was slightly higher than that of A/G type for the FRB transition types of SNP (Ts). However, the number of A/G type was slightly higher than that of C/T type for the VTB Ts, and the number of A/T type was the least for all transversion types of SNP (Tv). The value of Ts/Tv in FRB and VTB were 2.57 and 2.45, respectively. The AS events in FRB and VTB were 49 388 and 65 241, respectively. It mainly had five patterns of AS, of which the two largest proportions were transcription start site and transcription terminal site. Conclusion     The results of comparison and analysis of SNP and AS between the fresh and vitrified-thawed crossbred blastocysts of the yak provide valid data and theoretical basis for the following related gene function analysis and mining.

Key words: Crossbred yak, Blastocyst, Vitrification, RNA-Seq, Single nucleotide polymorphism, Alternative splicing